Evidence of Genetic Engineering in SARS-COV-2

Part 4 A Sting in the Tale of Kristian Andersen

When @K_G_Andersen "opened up" about the infamous email in which he stated "Eddie, Bob, Mike, and myself all find the [SARS-CoV2] genome inconsistent with expectations from evolutionary theory" he never quite told us exactly what he saw, but still he left a few clues.
In a response to questions from @nicholsonbaker8 he mentioned the FCS and the RBD, but also "a unique restriction enzyme site (BamHI) ...a higher level of conservation towards the end of the spike...other residues that had been observed to be important from research with SARS"
Since much of the focus to date has been on the FCS and RBD, let's instead take a look at a different region towards the end of the spike that had been of interest to SARS researchers - a "Cysteine-rich endo-domain" - Cysteine denoted by C:
In 2007, SARS researchers had tried exchanging some of these Cysteine (C) residues for Alanine (A) in parts of this region and discovered that cell fusion (merging and entry into the cell) was reduced by 50-60% when they did so.

https://t.co/iUEMYnldU3
The second half of the spike (S2) is far more conserved between coronaviruses than S1. On an amino acid basis there may be only a handful of mutations in several hundred bases. Looking at just the last 40, there's remarkable homology over time, species and geographic region.
One mutation stands out between SARS-COV-2 and others known previously. A single Ala is present in most viruses except SARS-COV-2 where it has been replaced by Cys.

Could this be a sign of engineering? If Cys->Ala reduces cell fusion, Ala->Cys might be expected to enhance it.
Astonishingly, on a nucleotide basis all 3 codons have mutated between SARS and SARS-COV-2. GCA has become TGT. This is extremely improbable under natural evolution. Occasional single nt mutations are expected, but here are three in one base-in a region that is highly conserved.
For Ala to mutate to Cys via point mutations it must first mutate to intermediate residues in steps. We might expect to find some of these in nature. Some codon combinations near C are stop codons, dead ends.

The path from Ala to Cys seems "inconsistent with natural evolution".
But are there any other coronaviruses with Cysteine in this position? Prior to SARS-COV-2 there were only two - ZC45 and ZC21, viruses sequenced by PLA researchers. These were identified (for different reasons) as the potential backbone for an engineered virus by @drlimengyan1.
Since the outbreak, new coronavirus discoveries have been springing up like weeds with features unseen prior to SARS-COV-2. Recently there's been a concerted effort to spam Genbank with fakes and frauds

Please check date added/modified if you find a CoV with similar mutations.
Link to earlier parts:

https://t.co/CeztISvFQN

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